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* [R](http://cran.us.r-project.org/) with [https://cran.r-project.org/web/packages/svglite/ svglite]: to do the differential expression analysis
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* [cairo-devel](https://www.cairographics.org/download/): 2d graphics library
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== Download the latest copy ==
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The latest version can be downloaded from the [https://mulcyber.toulouse.inra.fr/frs/?group_id=149 download page]
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# Download the latest copy
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The latest version can be downloaded from GitLab.
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== Extract the archive ==
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# Extract the archive
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[user@hostname:~] tar xzvf RNAbrowse_v1.3.tar.gz
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[user@hostname:~] cd RNAbrowse_v1.3
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== Configure the application ==
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# Configure the application
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You have then to edit the application.properties file.
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[global]
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# uncomment and set if not in the PATH
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... | ... | @@ -98,7 +98,7 @@ You have then to edit the application.properties file. |
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refseq_gi_from_accession = <path>/gene2accession_filter
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snpeff_config=<path>/snpEff/snpEff.config
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== Test your installation ==
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# Test your installation
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The application embed some test files, enter the following command lines to test the system:
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[user@hostname:~] python bin/ngspipelines_cli.py addinstance --instance-name myinstance
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[user@hostname:~] python ./bin/ngspipelines_cli.py load-rnaseqdenovo --instance-name myinstance --project-name DemoBrain --species "Dicentrarchus labrax" --species-common-name "SeaBass" --project-description "SeaBass brain transcriptome 500 examples contigs" \
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Once done, a browser should open a new window with the following display: <br />
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[[File:first_install_completed.png]]
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== Full test of your installation ==
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# Full test of your installation
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[user@hostname:~] python bin/ngspipelines_cli.py load-rnaseqdenovo @workflows/rnaseqdenovo/data/load/rnaseqdenovo.cfg
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[user@hostname:~] python bin/ngspipelines_cli.py runinstance --instance-name myinstance
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Once done, a browser should open a new window with the following display: <br />
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[[File:full_install_completed.png]]
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== Memory management ==
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# Memory management
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On real NGS data it is recommended to increase memory used by several softwares.
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=== Change memory in application.properties file. ===
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## Change memory in application.properties file.
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SGE exemple :
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[components]
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Blast.batch_options = -l mem=20G -l h_vmem=20G -q wflowq
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VariantPreprocess.batch_options = -l mem=25G -l h_vmem=25G -q wflowq
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tSNPannot.batch_options = -l mem=30G -l h_vmem=30G -q wflowq
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=== Change memory in workflows/rnaseqdenovo/__init__.py ===
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## Change memory in workflows/rnaseqdenovo/__init__.py
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Exemple line 147 to 150:
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def process(self):
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JAVA_LARGE_MEM = 20
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